Sightseeing
The places I often visit during my Tokyo tours
Asakusa (Senso-ji Temple and Asakusa Shrine)
https://www.japan-guide.com/e/e3004.html
Hamarikyu Gardens
https://www.japan-guide.com/e/e3025.html
Meiji Shrine
https://www.japan-guide.com/e/e3002.html
Omotesando (architecture)
This is the route I usually take.
https://goo.gl/maps/GzKnPNpWr9G2
 - TOKYU PLAZA Harakado
 - GYRE
 - Dior
 - Omotesando Hills (You should go inside)
 - TOD'S
 - Sasha Kanetanaka (high-class tea house)
 - PRADA
Shibuya
https://www.japan-guide.com/e/e3007.html
Imperial Palace East Gardens (*Closed on Mondays and Fridays)
https://www.japan-guide.com/e/e3018.html
Imperial Palace Sakurada-mon and Nijubashi Bridge
https://visit-chiyoda.tokyo/app/en/spot/detail/17
https://visit-chiyoda.tokyo/app/en/spot/detail/242
Tokyo Station (and KITTE building rooftop garden for views) 
https://www.japan-guide.com/e/e3037.html
Tokyo National Museum (*Closed on Mondays)
http://www.tnm.jp/?lang=en
Tsukiji Market
https://www.japan-guide.com/e/e3021.html
https://www.japan-guide.com/e/e2158.html